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CellExplorer: a graphical user interface and a standardized pipeline for visualizing and characterizing single neurons

View ORCID ProfilePeter C. Petersen, Joshua H. Siegle, View ORCID ProfileNicholas A. Steinmetz, Sara Mahallati, View ORCID ProfileGyörgy Buzsáki
doi: https://doi.org/10.1101/2020.05.07.083436
Peter C. Petersen
1Neuroscience Institute, Langone Medical Center, New York University, New York, NY 10016, USA
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  • For correspondence: gyorgy.buzsaki@nyumc.org petersen.peter@gmail.com
Joshua H. Siegle
4MindScope Program, Allen Institute, 615 Westlake Avenue North, Seattle, 98109, Washington, USA
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Nicholas A. Steinmetz
5Department of Biological Structure, University of Washington, Seattle, WA 98195, USA
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Sara Mahallati
6Institute of Biomedical Engineering, Krembil Research Institute, University of Toronto, Toronto, ON M5T 1M8, Canada
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György Buzsáki
1Neuroscience Institute, Langone Medical Center, New York University, New York, NY 10016, USA
2Department of Neurology, Langone Medical Center, New York University, New York, NY 10016, USA
3Center for Neural Science, New York University, New York, NY 10003, USA
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  • For correspondence: gyorgy.buzsaki@nyumc.org petersen.peter@gmail.com
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Abstract

The large diversity of neuron types of the brain, characterized by a unique set of electrophysiological characteristics, provides the means by which cortical circuits perform complex operations. To quantify, compare, and visualize the functional features of single neurons, we have developed the open-source framework, CellExplorer. It consists of three components: a processing module that calculates standardized physiological metrics, performs neuron type classification and detects putative monosynaptic connections, a flexible data structure, and a powerful graphical interface. The graphical interface makes it possible to explore any combination of pre-computed features at the speed of a mouse click. The CellExplorer framework allows users to process and relate their data to a growing collection of “ground truth” neurons from different genetic lines, as well as to tens of thousands of single neurons collected across our labs. We believe CellExplorer will accelerate the linking of physiological properties of single neurons in the intact brain to genetically identified types.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Major change to manuscript. New authors and figures.

  • https://cellexplorer.org/

  • https://buzsakilab.com/CellExplorer/CellExplorerMovie.mp4

  • https://github.com/petersenpeter/CellExplorer

  • https://buzsakilab.com/wp/database/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted December 24, 2020.
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CellExplorer: a graphical user interface and a standardized pipeline for visualizing and characterizing single neurons
Peter C. Petersen, Joshua H. Siegle, Nicholas A. Steinmetz, Sara Mahallati, György Buzsáki
bioRxiv 2020.05.07.083436; doi: https://doi.org/10.1101/2020.05.07.083436
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CellExplorer: a graphical user interface and a standardized pipeline for visualizing and characterizing single neurons
Peter C. Petersen, Joshua H. Siegle, Nicholas A. Steinmetz, Sara Mahallati, György Buzsáki
bioRxiv 2020.05.07.083436; doi: https://doi.org/10.1101/2020.05.07.083436

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